RetrogeneDB ID: retro_ocun_918

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:60638374..60638757(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SNX10
• Ensembl ID: ENSOCUG00000004744
• Aliases: None
• Description: sorting nexin 10 [Source:HGNC Symbol;Acc:14974]

Sequence

>retro_ocun_918
GTACAACTGCCCAAACTTCCATCTAAAAACCTCTTTTGCAACATGAACCCTCGCCAGCACGTGGATGAGTGTCACCAGGG
CTTGGAAGACTTCCTGTGAATAATCCTGCAGCGCGCACTCCTGCTGCTGGGCAGCAGCTTCCACCTTCTCTTGCAGAGCC
ATCCGAATGAAGAAGACACTGAGGTGCGTGTGTCCAAGATGACACACTCAGCGGAGGAGGCAATTCACAAGCTCTCGCTG
ATGACCAGACGGTTCCCCGAGGAAGATGAGGATGGGAAAAAGACCAGGATGCAGATTACGACTCAGAGGCTTCATTCTCT
GGGATTGGACACAGTAGTGATGATAGCAGCTCCCAGGCATGCAAAATAAGTCTATATCCACAG

Alignment

ORF - retro_ocun_918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRVPELPSKNLFFNMNNRQHVDQRRQGLEDFLRKVLQNALLLSDSSLHLFLQSHLAAADIDACVSGQTKY
          V..P.LPSKNLF.NMN.RQHVD...QGLEDFL...LQ.ALLL..SS.HL.LQSH....D....VS..T..
Retrocopy VQLPKLPSKNLFCNMNPRQHVDECHQGLEDFL*IILQRALLLLGSSFHLLLQSHPNEEDTEVRVSKMT-H

Parental  SVEEAIHKFALMNRRFPEEDEEGK-KDHDADYDSESSSSGLGHSSDDSSSHGCKISPDPQ
          S.EEAIHK..LM.RRFPEEDE.GK.KD.DADYDSE.S.SG.GHSSDDSSS..CKIS..PQ
Retrocopy SAEEAIHKLSLMTRRFPEEDEDGK<KDQDADYDSEASFSGIGHSSDDSSSQACKISLYPQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	64.79 RPM
SRP017611_kidney	0.00 RPM	11.96 RPM
SRP017611_liver	0.00 RPM	14.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_918 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_918 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_918 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000291	2 retrocopies	retro_chof_1983, retro_chof_445,
Myotis lucifugus	ENSMLUG00000000285	1 retrocopy	retro_mluc_488,
Mus musculus	ENSMUSG00000038301	1 retrocopy	retro_mmus_2736,
Oryctolagus cuniculus	ENSOCUG00000004744	1 retrocopy	retro_ocun_918 ,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,